Camelia, the Perl 6 bug

IRC log for #cdk, 2007-10-14

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All times shown according to UTC.

Time Nick Message
04:11 CIA-31 jmol: hansonr * r8402 /trunk/Jmol/src/org/jmol/sha​pebio/BackboneRenderer.java: version=11.3.32 bug fix: backbone not in state
04:15 CIA-31 jmol: hansonr * r8403 /branches/v11_2/Jmol/src/org/jmol/ (4 files in 2 dirs): 11.2.14 # bug fix: backbone not in state
04:43 CIA-31 jmol: hansonr * r8404 /trunk/Jmol/src/org/jmol/ (shapebio/BioShape.java viewer/StateManager.java): version=11.3.32 bug fix: backbone not in state
04:44 CIA-31 jmol: hansonr * r8405 /branches/v11_2/Jmol/src/org/j​mol/viewer/StateManager.java: 11.2.14 # bug fix: backbone not in state
04:48 CIA-31 jmol: hansonr * r8406 /branches/v11_2/Jmol/src/org/​jmol/viewer/Jmol.properties: 11.2.14 version
04:50 CIA-31 jmol: hansonr * r8407 /trunk/Jmol/src/org/jmol/viewer/Jmol.properties: 11.3.32 version
06:39 carsten joined #cdk
09:00 jbrefort joined #cdk
12:31 egonw joined #cdk
13:58 egonw joined #cdk
14:49 Nout joined #cdk
14:54 Nout hey people
14:54 Nout sorry i'm not really often here anymore, too busy at uni :/
15:21 egonw hi Nout
15:21 egonw same here
15:21 egonw did not have time to continue work on the new Controller2D
15:22 egonw will go offline now
15:22 egonw busy weekend too
16:02 carsten joined #cdk
16:22 jbrefort joined #cdk
17:33 CIA-31 jmol: hansonr * r8408 /trunk/Jmol/src/org/jmol/ (11 files in 3 dirs): (log message trimmed)
17:33 CIA-31 jmol: version=11.3.32
17:33 CIA-31 jmol: # new feature: getproperty stateinfo TYPE
17:33 CIA-31 jmol: # where TYPE is one of:
17:33 CIA-31 jmol: #
17:33 CIA-31 jmol: # colorState
17:33 CIA-31 jmol: # dataState
17:39 egonw joined #cdk
18:01 CIA-31 cdk: egonw * r9042 /branches/cdk-1.0.x/patches.txt: Updated; going to try to get a 1.0.2 released
18:05 CIA-31 cdk: egonw * r9043 /branches/cdk-1.0.x/src/org/openscience/cdk/te​st/layout/StructureDiagramGeneratorTest.java: Merged r8691: Added test case for bug #1772609 'NPE with bridged rings in SDG/RingPlacer'.
18:07 CIA-31 cdk: egonw * r9044 /branches/cdk-1.0.x/src/org/openscience/cdk/isom​orphism/matchers/QueryAtomContainerCreator.java: Merged r8697: Add a method to the query atom container creator which creates an queryatomcontainer. This replaces each pseudoatom to an anyatom.
18:09 CIA-31 cdk: egonw * r9045 /branches/cdk-1.0.x/src/ (2 files in 2 dirs): Merged r8699 and r8700: Added test file by Volker (see cdk-user) for the shortest path problem; JUnit test provided by Volker Haehnke (haehnke - bioinformatik uni-frankfurt de), somewhat rewritten.
18:11 CIA-31 cdk: egonw * r9046 /branches/cdk-1.0.x/src/org/opens​cience/cdk/graph/PathTools.java: Merged r8701: Renamed a variable to comply with http://en.wikipedia.org/wiki/Dijkstra's_algorithm
18:13 CIA-31 cdk: egonw * r9047 /branches/cdk-1.0.x/src/org/openscience/cdk/ (smiles/SmilesParser.java test/smiles/SmilesParserTest.java): Merged r8751: Bug fixes for bugs #1783367 'SmilesParser incorrectly assigns double bonds' and #1783381 'SmilesParser uses Molecule instead of IMolecule'. Test case for bug #1783367.
18:15 CIA-31 cdk: egonw * r9048 /branches/cdk-1.0.x/src/org/openscience/cdk/ (3 files in 2 dirs): Merged r8754 and r8773: Fix and test case for bug #1783547 and #1783546 'Lost aromaticity in SmilesParser with Biphenyl and Benzene'
18:16 CIA-31 cdk: egonw * r9049 /branches/cdk-1.0.x/src/org/opensci​ence/cdk/io/MDLRXNV2000Reader.java: Merged r8774: Add a MDL RXN reader which uses the MDLV2000Reader instead of the MDLReader
18:23 CIA-31 cdk: egonw * r9050 /branches/cdk-1.0.x/src/org/openscience/cdk/ (5 files in 4 dirs): Merged r8775, r8776, r8777: bug fixes for #150354 #1783774 #1778479 in the SmilesParser, SmilesGenerator and MDLWriter/PseudoAtom.
18:25 CIA-31 cdk: egonw * r9051 /branches/cdk-1.0.x/src/org/openscien​ce/cdk/smiles/smarts/SMARTSParser.jj: Merged r8791: Code for v,mass atom two digits mass atom and exception handeling
18:26 CIA-31 cdk: egonw * r9052 /branches/cdk-1.0.x/src/org/openscience/cdk/ (io/MDLV2000Reader.java test/io/MDLV2000ReaderTest.java): Merged r8800: Fixed reading of MDL molfiles with exactly 12 columns (==valid) in the bond block
18:29 CIA-31 cdk: egonw * r9053 /branches/cdk-1.0.x/src/org/openscie​nce/cdk/qsar/descriptors/molecular/ (4 files): Merged r8802: Made a little more memory efficient by removing unnesscary cloning operations
18:29 CIA-31 cdk: egonw * r9054 /branches/cdk-1.0.x/src/org/openscience/cdk/qs​ar/descriptors/molecular/BCUTDescriptor.java: Merged r8803: Fixed it so that we make a deep copy of the input molecule
18:30 CIA-31 cdk: egonw * r9055 /branches/cdk-1.0.x/src/org/openscie​nce/cdk/qsar/descriptors/molecular/ (2 files): Merged r8809: Added code to work on a local copy of theinput molecule
18:32 CIA-31 cdk: egonw * r9056 /branches/cdk-1.0.x/src/org/opensc​ience/cdk/qsar/descriptors/molecul​ar/MomentOfInertiaDescriptor.java: Merged r8811: Updated Javadocs
18:35 CIA-31 cdk: egonw * r9057 /branches/cdk-1.0.x/src/org/ope​nscience/cdk/qsar/descriptors/ (17 files in 4 dirs): Merged 8824 8821 8820 8819 8817 8816: Added code to properly work on a local copy
19:32 carsten joined #cdk
19:32 egonw hi carsten
19:33 carsten moin
19:33 carsten rev_egonw: hey, the chemspider thing is cool!
19:34 rev_egonw which chemspider thing?
19:34 rev_egonw the workflow?
19:34 carsten rev_egonw: your blog
19:34 carsten now, the database
19:34 carsten http://www.chemspider.com/Search.aspx
19:38 rev_egonw ah...
19:39 CIA-31 cdk: egonw * r9058 /branches/cdk-1.0.x/src/ (5 files in 5 dirs): Removed some J5 talk
19:39 CIA-31 cdk: egonw * r9059 /branches/cdk-1.0.x/patches.txt: Updated up to 8843
19:44 CIA-31 cdk: egonw * r9060 /branches/cdk-1.0.x/src/org/open​science/cdk/AtomContainer.java: Merged 8848: Fixed an ArrayIndexOutOfBoundsException
19:46 CIA-31 cdk: egonw * r9061 /branches/cdk-1.0.x/src/org/openscience/cdk/ (3 files in 3 dirs): Merged r8850: Removed tainted code (unclear license, no statement) and classes depending on it (closes #1701312)
19:47 CIA-31 cdk: egonw * r9062 /branches/cdk-1.0.x/src/org/openscience/cdk/ (3 files in 2 dirs):
19:47 CIA-31 cdk: Merged r8881: The cause for hard to reproduce StructureDiagramGenerator bugs was
19:47 CIA-31 cdk: the undeterministic order of the rings returned by SSSRFinder.findSSSR(). The
19:47 CIA-31 cdk: rings are now sorted by a new method AtomContainerSetManipulator.sort() which
19:47 CIA-31 cdk: uses the new class AtomContainerComparator. Also the safetyCounters in the SDG
19:47 CIA-31 cdk: were made effective. This should prevent all hangs of the SDG in future.
19:50 CIA-31 cdk: egonw * r9063 /branches/cdk-1.0.x/src/org/openscience/cdk/to​ols/manipulator/AtomContainerComparator.java: Merged r8883: Added SVN keywords to the copyright comment.
19:51 CIA-31 cdk: egonw * r9064 /branches/cdk-1.0.x/src/dat​a/templates/diamantane.cml: Merged r8884: The molecule ID of diamantane.cml incorrectly was 'cubane'
20:04 CIA-31 cdk: egonw * r9065 /branches/cdk-1.0.x/src/ (6 files in 3 dirs): Merged r8885 and r8886: This commit fixes bugs #1784850, #1677912 and #1714794
20:11 CIA-31 cdk: egonw * r9066 /branches/cdk-1.0.x/src/org/ope​nscience/cdk/io/PDBWriter.java: Merged r8901: Added a statement to say that the current PDBWriter does not write protein structures
20:12 CIA-31 cdk: egonw * r9067 /branches/cdk-1.0.x/src/org/ope​nscience/cdk/math/Primes.java: Merged 8903: Applied patch by Bala <bkbsub@gmail.com>: more integers
20:14 CIA-31 cdk: egonw * r9068 /branches/cdk-1.0.x/src/org/openscience/cdk​/charges/GasteigerPEPEPartialCharges.java: Merged r8911: Added correct bibliography into javaDoc
20:37 CIA-31 jmol: hansonr * r8409 /trunk/Jmol/src/org/jmol/ (13 files in 4 dirs):
20:37 CIA-31 jmol: version=11.3.32
20:37 CIA-31 jmol: # code(II): ModelSet extends ModelCollection extends BondCollection extends AtomCollection
20:37 CIA-31 jmol: #
20:37 CIA-31 jmol: # bug fix: dipoles moved back into shape from shapespecial
20:47 CIA-31 jmol: hansonr * r8410 /trunk/Jmol/src/org/jmol/viewer/Eval.java:
20:55 CIA-31 cdk: egonw * r9069 /branches/cdk-1.0.x/src/org/openscience/cdk/ (19 files in 6 dirs): Merged 8924-8927: SMARTS updates
20:57 CIA-31 cdk: egonw * r9070 /branches/cdk-1.0.x/src/org/openscience/cdk/isomo​rphism/matchers/smarts/RecursiveSmartsAtom.java: Merged r8940: Fixed a recursive smarts matching bug found by Rajarshi
21:00 CIA-31 cdk: egonw * r9071 /branches/cdk-1.0.x/src/org/opensc​ience/cdk/qsar/descriptors/molecul​ar/PetitjeanNumberDescriptor.java: Merged 8942: Updated to take into accout the pathological case of a single atom
21:02 CIA-31 cdk: egonw * r9072 /branches/cdk-1.0.x/src/org/openscience/cdk/ (math/Primes.java test/math/PrimesTest.java): Merged 8960 and 8961: Updated the JavaDoc for the recently added primes. Fixed the test for the recently added primes, and split up two situations into separate tests.
21:06 CIA-31 jmol: hansonr * r8411 /trunk/Jmol/src/org/jmol/viewer/ (Eval.java Jmol.properties): version=11.3.32 # bug fix: zoomto (atomExpression) 0 # zooms to 2x
21:08 CIA-31 jmol: hansonr * r8412 /branches/v11_2/Jmol/src/org/jmol/viewer/ (Eval.java Jmol.properties): version=11.2.14 # bug fix: zoomto (atomExpression) 0 # zooms to 2x
21:14 CIA-31 cdk: egonw * r9073 /branches/cdk-1.0.x/doc/refs/cheminf.bibx: Missing ref: merged from trunk, unknown commit
21:14 CIA-31 cdk: egonw * r9074 /branches/cdk-1.0.x/src/org/openscience/cdk/isomo​rphism/matchers/smarts/RecursiveSmartsAtom.java: Merged 9041: Fixed bug when reuse the same QueryAtomContainer with RecursiveSmarts
21:22 CIA-31 cdk: egonw * r9075 /branches/cdk-1.0.x/ (build.props patches.txt): Ready for 1.0.2?
21:28 CIA-31 cdk: egonw * r9076 /branches/cdk-1.0.x/BUGS: Snapshot of JUnit test results for the stable modules
21:30 CIA-31 cdk: egonw * r9077 /branches/cdk-1.0.x/changelog.txt: New changelog
21:31 CIA-31 jmol: hansonr * r8413 /trunk/Jmol/src/org/jmol/viewer/ (3 files): version=11.3.32 # bug fix: zoomto cancels slabbing
21:32 egonw OK, bed time
21:33 CIA-31 jmol: hansonr * r8414 /branches/v11_2/Jmol/src/org/jmol/viewer/ (3 files): version=11.2.14 # bug fix: zoomto cancels slabbing
21:47 CIA-31 jmol: hansonr * r8415 /trunk/Jmol/src/org/jmol/ (modelset/Atom.java viewer/Jmol.properties): version=11.3.32 # bug fix: vibration disabled in 11.3.31
22:26 CIA-31 jmol: hansonr * r8416 /trunk/Jmol/src/org/jmol/ex​port/DipolesGenerator.java:
22:26 CIA-31 jmol: version=11.3.32
22:26 CIA-31 jmol: # bug fix: dipoles moved back into shape from shapespecial

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